Real-time observation of a single DNA digestion by lambda exonuclease under a fluorescence microscope field

Nucleic Acids Res. 2001 Aug 15;29(16):E79. doi: 10.1093/nar/29.16.e79.

Abstract

A fluorescence microscopy technique has been developed to visualize the behavior of individual DNA and protein molecules. Real-time direct observation of a single DNA molecule can be used to investigate the dynamics of DNA-protein interactions, such as the DNA digestion reaction by lambda exonuclease. In conventional methods it is impossible to analyze the dynamics of an individual lambda exonuclease molecule on a DNA because they can only observe the average behavior of a number of exonuclease molecules. Observation of a single molecule, on the other hand, can reveal processivity and binding rate of an individual exonuclease molecule. To evaluate the dynamics of lambda exonuclease, a stained lambda DNA molecule with one biotinylated terminal was fixed on an avidin-coated coverslip and straightened using a d.c. electric field. Microscopic observation of digestion of a straightened DNA molecule by lambda exonuclease revealed that the DNA digestion rate was approximately 1000 bases/s and also demonstrated high processivity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Avidin / metabolism
  • Bacteriophage lambda / enzymology*
  • Bacteriophage lambda / genetics*
  • Benzoxazoles / metabolism
  • Biotinylation
  • DNA, Viral / metabolism*
  • DNA-Binding Proteins / metabolism
  • Electromagnetic Fields
  • Exodeoxyribonucleases / metabolism*
  • Fluorescent Dyes / metabolism
  • Intercalating Agents / metabolism
  • Kinetics
  • Microscopy, Fluorescence / methods*
  • Protein Binding
  • Quinolinium Compounds / metabolism
  • Time Factors
  • Viral Proteins

Substances

  • Benzoxazoles
  • DNA, Viral
  • DNA-Binding Proteins
  • Fluorescent Dyes
  • Intercalating Agents
  • Quinolinium Compounds
  • Viral Proteins
  • Avidin
  • 1,1'-((4,4,7,7-tetramethyl)-4,7-diazaundecamethylene)bis-4-(3-methyl-2,3-dihydro(benzo-1,3-oxazole)-2-methylidene)quinolinium
  • Exodeoxyribonucleases
  • exo protein, Bacteriophage lambda